RELATED: 60 Percent of Virus Experts Wouldn’t Do These 6 Things Right Now, Data Shows.ae0fcc31ae342fd3a1346ebb1f342fcb According to the agency’s latest biweekly report detailing virus sequencing for the two-week period ending on Sept. 11, the B.1.617.2 lineage of the highly contagious variant is now responsible for 99.4 percent of COVID cases in the U.S., while two other Delta lineages made up 0.2 and 0.1 percent. The figures represent a stark rise from mid-June when the strain constituted just over a quarter of all cases after being first discovered in the U.S. in April, The New York Times reports. After causing major outbreaks across India and the U.K., the infamous variant has been largely responsible for a summer-long surge across the U.S. that saw significant previous progress against the virus erased. “It’s not unexpected, because it’s more transmissible, but it is also a strong reminder that we need to have continuous vigilance,” Saskia Popescu, PhD, an epidemiologist and assistant professor at George Mason University, told The Times. The virus has notably become a source of concern over its ability to cause breakthrough infections in fully vaccinated. Fortunately, studies have found the shots still appear to be highly effective in preventing severe disease or death in those who have received all necessary doses. But the rise of the variant has also led to a significant spike in hospitalizations nationwide—especially among a part of the population that was previously less affected by the virus. “This virus is really going for the people who are not vaccinated,” Edith Bracho-Sanchez, PhD, associate professor of pediatrics at Columbia University Irving Medical Center, told CNN. “And among those people are children who don’t qualify for the vaccine and children and teens who qualify but are choosing not to get it.” RELATED: The 5 Most Common Signs You Caught Delta If You’re Vaccinated, Study Says. Some experts have predicted that the Delta-fueled outbreaks in states with low vaccination rates may finally be past their peaks. But others remained cautious, pointing out that a change in seasons may see a new wave of cases rise in some areas as children returned to classrooms. “I really hope I’m wrong here, I pray to God I’m wrong…but I fear our schools are going to become the flash forest fire for the virus for the upcoming weeks,” Michael T. Osterholm, PhD, MPH, an epidemiologist and the director of the Center for Infectious Disease Research and Policy (CIDRAP) and the University of Minnesota, said during an episode of his weekly podcast, Osterholm Update on Sept. 9. “Kids, New York, and L.A.—those will determine where we go,” the epidemiologist warned. The highly contagious variant has led other experts to reassess their outlook on the pandemic’s timeline. During a phone interview with CNBC on Sept. 15, Stephen Hoge, president of vaccine manufacturer Moderna, said the Delta variant is “just so good at infecting people and replicating that it raises the bar on how good vaccines have to be,” adding that “it’s actually shown some of the weaknesses that [vaccines] have earlier than you might expect.” RELATED: For more up-to-date information, sign up for our daily newsletter. Ultimately, experts say the Delta variant is a harsh reminder that the pandemic is still far from over and that we shouldn’t underestimate the latest version of the viral enemy. “The biggest piece is, ‘Don’t let your guard down.’ We need continuous surveillance, genomic sequencing, access to testing, and public health interventions,” Popescu told The Times, adding that masks and vaccinations could go a long way in preventing the spread of the virus. “We have transmission occurring with very limited exposure, and that means that, for example, times without a mask, when you are out and around others, become much more of a risk.” RELATED: If You Got This Vaccine, You May Be More Protected Against Delta.